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@@ -19,6 +19,38 @@ deploy GN2 and dependencies as a self contained unit on any machine. The database can be run separately as well as the source tree (for developers). See the [installation docs](doc/README.org). +## Configuration + +GeneNetwork2 comes with a [default configuration file](./etc/default_settings.py) +which can be used as a starting point. + +The recommended way to deal with the configurations is to **copy** this default configuration file to a location outside of the repository, say, + +```sh +.../genenetwork2$ cp etc/default_settings.py "${HOME}/configurations/gn2.py" +``` + +then change the appropriate values in the new file. You can then pass in the new +file as the configuration file when launching the application, + +```sh +.../genenetwork2$ bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run> +``` + +The other option is to override the configurations in `etc/default_settings.py` +by setting the configuration you want to override as an environment variable e.g. +to override the `SQL_URI` value, you could do something like: + +```sh +.../genenetwork2$ env SQL_URI="mysql://<user>:<passwd>@<host>:<port>/<db_name>" \ + bin/genenetwork "${HOME}/configurations/gn2.py" <command-to-run> +``` + +replacing the placeholders in the angle brackets with appropriate values. + +For a detailed breakdown of the configuration variables and their use, see the +[configuration documentation](doc/configurations.org) + ## Run Once having installed GN2 it can be run through a browser @@ -59,6 +91,20 @@ asserts sprinkled in the code base. Right now, the only tests running in CI are unittests. Please make sure the existing unittests are green when submitting a PR. +From the root directory of the repository, you can run the tests with something +like: + +```sh +env GN_PROFILE=~/opt/gn-latest SERVER_PORT=5300 \ + SQL_URI=<uri-to-override-the-default> \ + ./bin/genenetwork2 ./etc/default_settings.py \ + -m unittest -v +``` + +In the case where you use the default `etc/default_settings.py` configuration file, you can override any setting as demonstrated with the `SQL_URI` setting in the command above. + +In order to avoid having to set up a whole host of settings every time with the `env` command, you could copy the `etc/default_settings.py` file to a new location (outside the repository is best), and pass that to `bin/genenetwork2` instead. + See [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/doc/docker-container.org) for more details. |